1JKU

Crystal Structure of Manganese Catalase from Lactobacillus plantarum

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Crystal structure of manganese catalase from Lactobacillus plantarum.

Barynin, V.V., Whittaker, M.M., Antonyuk, S.V., Lamzin, V.S., Harrison, P.M., Artymiuk, P.J., Whittaker, J.W.

(2001) Structure 9: 725-738

  • DOI: https://doi.org/10.1016/s0969-2126(01)00628-1
  • Primary Citation of Related Structures:  
    1JKU, 1JKV

  • PubMed Abstract: 

    Catalases are important antioxidant metalloenzymes that catalyze disproportionation of hydrogen peroxide, forming dioxygen and water. Two families of catalases are known, one having a heme cofactor, and the other, a structurally distinct family containing nonheme manganese. We have solved the structure of the mesophilic manganese catalase from Lactobacillus plantarum and its azide-inhibited complex.

    • Organizational Affiliation: 

    The Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, S10 2TN, Sheffield, United Kingdom. v.barynin@sheffield.ac.uk


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
pseudocatalase
A, B, C, D, E
A, B, C, D, E, F
266Lactiplantibacillus plantarumMutation(s): 0 
EC: 1.11.1.6
UniProt
Find proteins for P60355 (Lactiplantibacillus plantarum)
Explore P60355 
Go to UniProtKB:  P60355
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60355
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MN3
Query on MN3
Download Ideal Coordinates CCD File 
CA [auth D]
DA [auth D]
IA [auth E]
JA [auth E]
K [auth A]
CA [auth D],
DA [auth D],
IA [auth E],
JA [auth E],
K [auth A],
L [auth A],
OA [auth F],
PA [auth F],
Q [auth B],
R [auth B],
W [auth C],
X [auth C]
MANGANESE (III) ION
Mn
MMIPFLVOWGHZQD-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
EA [auth E]
G [auth A]
KA [auth F]
M [auth B]
S [auth C]
EA [auth E],
G [auth A],
KA [auth F],
M [auth B],
S [auth C],
Y [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
OH
Query on OH
Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
FA [auth E]
GA [auth E]
H [auth A]
AA [auth D],
BA [auth D],
FA [auth E],
GA [auth E],
H [auth A],
HA [auth E],
I [auth A],
J [auth A],
LA [auth F],
MA [auth F],
N [auth B],
NA [auth F],
O [auth B],
P [auth B],
T [auth C],
U [auth C],
V [auth C],
Z [auth D]
HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.72α = 90
b = 96.42β = 106.88
c = 106.69γ = 90
Software Package:
Software NamePurpose
DMmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description